Senior Project Week 1 (4/2-4/5)

This week was my first week working at the NYU Center for Soft Matter Research. On Tuesday, my first day, I was given a tour of the facilities and introduced to the work that each of the team members was doing. I also learned more about the specific project I would be working on, which involves creating droplets out of a soap-like substance and coating them with different types of DNA, then examining how the droplets interact with each other and what shapes they form. Specifically, we decided to try and create long chains of droplets that are a single droplet wide. 

On Wednesday, I still didn’t have the lab training I needed to be able to perform experiments myself, so I observed as the team member I was working with showed me how to prepare the droplets that we would be examining. This process involves mixing two types of DNA with a buffer solution in 2 different tubes, and also incorporating two types of fluorescent dyes so that the droplets would be visible and distinguishable under a microscope. I was also taught how to use the microscope, which shows the droplets as a sea of blue and yellow bubbles that form chains and other shapes, and also takes time-lapse videos of the droplets forming the chains.

In order to manipulate the binding of the droplets, a couple of steps need to be taken. First, the temperature of the sample needs to be heated to around 50 degrees Celsius in order to break apart all of the bonds between the droplets, and then the droplets need to be forced into a linear alignment by a magnet, and then the sample can be cooled, allowing the droplets to rebind, but in a more linear structure, allowing long chains to be formed. Repeating this process over and over allows for different ways to create long chains to be explored. 

On Thursday, we continued experimenting with the droplets, which is when we discovered a problem. In order to ensure that most of the droplet chains are only a single droplet long, the valence, or number of possible binding sites, of the droplets needs to be minimized. This is done by reducing the concentration of DNA mixed into the droplet sample. The problem with this is, in a sample of droplets, there is always a risk of two droplets merging together, or coalescing, and this risk becomes greater the less saturated the droplet surface is with DNA. Essentially, a sample full of droplets that has coalesced is unusable, so we decided that, in the future, we should add more types of DNA to the surface, but make it DNA that cannot bind to DNA on other droplets in the sample. I was also able to complete my lab training on Thursday. 

On Friday, most of the morning was spent in a group meeting with the other members of the team. Although it was briefly interrupted by the earthquake, I got to hear even more about the work that other team members were doing, which was very interesting. I also received some valuable feedback on my project, which included a suggestion to instead of trying to maximize the length of the droplet chains, focus on creating chains of random sequences and examining the subsequent folding structure after removing the magnet. With this in mind, we did some more experimenting with droplet sequences under the microscope before heading home for the weekend.